CRISPR start-up Graphite Bio launches with $45 million for targeted DNA integration

Graphite Bio, the latest start-up dedicated to CRISPR gene editing, has launched with $45 million in series A financing and an experimental CRISPR therapy that it plans to begin testing in humans in early 2021.

The San Francisco–based company is moving quickly, thanks to the work of academic cofounder Matthew Porteus, a pediatric hematologist and gene-editing researcher whose lab at Stanford University has spent the past 4 years improving and refining a technique that uses CRISPR to correct the mutation responsible for sickle cell disease.

Graphite is not the first gene-editing company with plans to tackle sickle cell, but its founders, and investors from Versant Ventures and Samsara BioCapital, contend that the start-up has the technology and knowhow to insert new DNA into genomes more accurately and efficiently than its competitors.

Sickle cell disease is caused by a single mutation in the gene for β-globin—a component of adult hemoglobin, which ferries oxygen throughout the body.

In theory, the disease could be cured by fixing this mutation in hematopoietic stem cells, which make our hemoglobin-filled red blood cells. “The concept of this is not new,” says Graphite CEO Josh Lehrer, who was recruited from his former post as chief medical officer of Global Blood Therapeutics. But directly fixing this genetic mutation has proven harder than expected.

As a rule of thumb, the gene-editing tool CRISPR-Cas9 is better at breaking things than fixing them. That’s led several firms—including Crispr Therapeutics, Editas Medicine, and Intellia Therapeutics—to devise clever workarounds. These companies are all trying to use CRISPR-Cas9 to turn on production of fetal hemoglobin by breaking a gene that normally keeps fetal hemoglobin production switched off in adults. It’s an elegant solution, and Lehrer says the approach is encouraging. “But the definitive way to cure this disease is to just fix the problem,” he adds, which means replacing the mutation with the correct genetic code.

Graphite calls the fixing technique targeted DNA integration. Fixing the mutation in the β-globin gene requires three components: the Cas9 enzyme to cut the DNA, the guide RNA to tell Cas9 where to cut, and so-called donor DNA, which contains the sequence of a β-globin gene without the sickle cell mutation. A cell’s natural DNA repair machinery can use the donor DNA as a blueprint for repairing the break made by Cas9, and in doing so, can overwrite the sickle cell mutation.

Porteus published a demonstration of the technique back in 2016 in a project led by his former postdoctoral researcher Daniel Dever—who is also a Graphite cofounder. Labs previously struggled to correct DNA mutations in more than a few percent of cells. In 2016, Dever’s project corrected a surprisingly high 20–30% of cells. For the past 4 years, Porteus’s lab has been plugging away at boosting those numbers, which he says are now as high as 60–80% in the lab. Graphite is shooting for over 50% during clinical manufacturing.

Other papers published by Porteus’s lab offer some clues about how the group improved its editing efficiency. His lab found that using a delivery virus called adeno-associated virus 6 (AAV6) helps boost the integration of the donor DNA into the break made by Cas9. And in 2018, his group reported using a modified version of Cas9, called HiFi Cas9, to improve editing efficiency.

Jeral Davis, a managing director of Versant—the founding investor in Graphite—explains that Graphite is based on several small advances that together make high rates of targeted DNA integration possible. How the Cas9 enzyme, the guide RNA, and the donor DNA are delivered, as well as how the edited cells are processed, are all key, he says. “It is not a single ‘aha’ discovery.”

A “distinguishing feature” of Graphite, Porteus says, is its running start on clinical-scale manufacturing, which he’s already begun at Stanford. “I don’t think that is normal for an academic program or a company at this stage to have that in place,” he says. Expertise from stem-cell and gene-therapy veteran Maria Grazia Roncarolo, a Stanford professor and Graphite cofounder, helps as well.

Graphite has some gene-editing tricks that it’s not disclosing yet, including how to push cells into different states where they become more or less likely to integrate donor DNA. “To be honest, we haven’t published on the 4 years of work that’s gone into developing this program,” Porteus says.

The manuscript describing the work is on his desk, he adds, but the launch of Graphite and the upcoming clinical trial have been priorities. The firm plans on filing an Investigational New Drug Application—the formal request for permission to begin a clinical trial—with the US Food and Drug Administration by the end of the month.

Crispr Therapeutics and Vertex Pharmaceuticals are already working together to test their own CRISPR therapy for sickle cell in the clinic, based on the fetal hemoglobin boosting strategy. Early data from the first person to receive the therapy suggests it might be safe and effective, but it’s too early to say for sure.

Graphite has undisclosed programs beyond sickle cell that could enter clinical trials within 12–18 months. Carlo Rizzuto, a partner at Versant Ventures, says Graphite’s initial focus is on genetic diseases that can be cured by editing hematopoietic stem cells. But he also envisions “a broad range of platforms,” including using CRISPR to engineer hematopoietic stem cells that secrete therapeutic proteins and engineering other types of cells for immunotherapy.